Would "well done" also apply to a case, in which the performer of the action, the one for which he is receiving a praise, is still performing it at the moment of receiving the praise, in other words, when he is not done yet?

For example:

Dad: "Okay, now start jumping over these obstacles and keep doing it
for 5 minutes"

Speaking entirely personally, I have to contradict the existing two answers (at time of writing) and say that in British English at least, "well done" is an idiomatic phrase, has lost a great deal of its literal meaning, to the extent that it can be used to refer to an activity that is underway, and perhaps even an activity yet to begin.

The scenario in the question seems perfectly natural to me:

Dad: "Okay, now start jumping over these obstacles and keep doing it
for 5 minutes"

Son: "Okay, Dad!"

Dad (1 minute later): "Well done. You are doing really well!"

I would also not find the following exchange jarring:

Son: I'm going to do my homework before dinner

Dad: Well done.

This is clearly nonsense in terms of the literal meaning of the words, but colloquially it is commonplace in the UK.